4MSX

Crystal structure of an essential yeast splicing factor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The crystal structure of S. cerevisiae Sad1, a catalytically inactive deubiquitinase that is broadly required for pre-mRNA splicing.

Hadjivassiliou, H.Rosenberg, O.S.Guthrie, C.

(2014) Rna 20: 656-669

  • DOI: 10.1261/rna.042838.113

  • PubMed Abstract: 
  • Sad1 is an essential splicing factor initially identified in a genetic screen in Saccharomyces cerevisiae for snRNP assembly defects. Based on sequence homology, Sad1, or USP39 in humans, is predicted to comprise two domains: a zinc finger ubiquitin ...

    Sad1 is an essential splicing factor initially identified in a genetic screen in Saccharomyces cerevisiae for snRNP assembly defects. Based on sequence homology, Sad1, or USP39 in humans, is predicted to comprise two domains: a zinc finger ubiquitin binding domain (ZnF-UBP) and an inactive ubiquitin-specific protease (iUSP) domain, both of which are well conserved. The role of these domains in splicing and their interaction with ubiquitin are unknown. We first used splicing microarrays to analyze Sad1 function in vivo and found that Sad1 is critical for the splicing of nearly all yeast intron-containing genes. By using in vitro assays, we then showed that it is required for the assembly of the active spliceosome. To gain structural insights into Sad1 function, we determined the crystal structure of the full-length protein at 1.8 Å resolution. In the structure, the iUSP domain forms the characteristic ubiquitin binding pocket, though with an amino acid substitution in the active site that results in complete inactivation of the enzymatic activity of the domain. The ZnF-UBP domain of Sad1 shares high structural similarly to other ZnF-UBPs; however, Sad1's ZnF-UBP does not possess the canonical ubiquitin binding motif. Given the precedents for ZnF-UBP domains to function as activators for their neighboring USP domains, we propose that Sad1's ZnF-UBP acts in a ubiquitin-independent capacity to recruit and/or activate Sad1's iUSP domain to interact with the spliceosome.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SAD1
A
482Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SAD1
Find proteins for P43589 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P43589
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.184 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 139.315α = 90.00
b = 139.315β = 90.00
c = 86.737γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
PHENIXrefinement
PHASERphasing
Blu-Icedata collection

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-16
    Type: Initial release
  • Version 1.1: 2014-05-07
    Type: Database references